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\title{HMM for Bioinformatics}
\author{\textbf{Pawe{\l} B{\l}a{\.z}ej}\\
Department of Genomics, Faculty of Biotechnology,\\
blazej@smorfland.uni.wroc.pl}

\begin{document}
\begin{frame}
\titlepage
\end{frame}
\begin{frame}
\frametitle{piece of literature}
\begin{itemize}
\item <1-> W.H. Majoros, ``Methods for Computational Gene Prediction'', Cambridge University Press 2007;
  \item <2-> T. Koski, ``Hidden Markov Models for Bioinformatics'', Kluwer Academic Publishers 2001.
\item <3->  \url{http://smorfland.uni.wroc.pl/~blazej/HMM/}  
  \end{itemize}
\end{frame}
\begin{frame}
\frametitle{Getting started}
\begin{block}{}
\begin{enumerate}
\item<1->Mathematically trained individuals prefer their problems to be stated simply and precisely;
\item<2-> To persons with a mathematical training, biology appears to be bewildering array of terminology and conventions;
\end{enumerate}
\end{block}
\end{frame}

\begin{frame}
\frametitle{Getting started}

\begin{block}{}
\begin{enumerate}
\item <1-> The students are advised not to treat everything which will be said here as being "biologically true".
\item<2-> All the biological statements that will appear during this lecture are "probably approximately correct". 
\end{enumerate}
\end{block}

\end{frame}

\begin{frame}
  \frametitle{The first}
\begin{block}{Statement}
  All life on this planet depends on three types of molecule DNA, RNA and proteins,
\end{block}  
\end{frame}  

\begin{frame}
  \frametitle{The second}
  \begin{block}{Statement}
    DNA is a vast library describing how the cell works
  \end{block}  
\end{frame}  

\begin{frame}
\begin{block}{Statement}
RNA acts to transfer certain short pieces of this library to different places in the cell at which point those smaller volumes of information are used as a templates to synthetize proteins.
\end{block}
\end{frame}

\begin{frame}
\begin{block}{Statement}
Proteins form enzymes that perform biochemical reactions, send signals to other cells, form the body's major component and otherwise perform the actual work of the cell.   
\end{block}

\end{frame}  

\begin{frame}
  \frametitle{Short history of DNA and RNA}
 \begin{enumerate} 
 \item <1-> 1869 -- DNA was discovered by Johann Friedrich Miescher;
 \item <2-> By the eaerly 1900s it was shown that DNA was a long molecule consisting of four types of bases;
 \item <3-> By the 1920s, nucleid acids were grouped into two classes called DNA and RNA, that differ slightly intheir base composition.    
\end{enumerate}  
\end{frame}
\begin{frame}
\frametitle{Short history of DNA and RNA}
\begin{block}{fact 1.}
Ironically, for a long time biologists paid a little attention to DNA. 
\end{block}  
\begin{block}{Important date}
1940 -- Oswald Avery and colleagues proved that genes indeed reside on DNA.
\end{block}
\end{frame}
\begin{frame}
  \frametitle{What is the structure of DNA?}
\begin{enumerate}  
\item <1-> 1950 -- Erwin Chargraff discovered one-to-one ratio of the adynine-to-thymine and guanine-to-citosine in DNA;
\item <2-> 1951 -- Maurice Wilkins and Rosalind Franklin obtained sharp x-ray images of DNA;
\item <2-> 1953 -- James Watson and Francis Crick determined the double helical structure of a DNA molecule.  
\end{enumerate}  
\end{frame}
\begin{frame}
\frametitle{Human Genomic Project -- 2001 }
The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome (more than three billion). The "genome" of any given individual is unique; mapping the "human genome" involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.

\end{frame}

\begin{frame}
  \frametitle{Rosetta Stone}
 \begin{center} 
\includegraphics[width=0.5\linewidth]{rysunki/rosetta.png}
\end{center}

  
\end{frame}  

\begin{frame}
  \frametitle{DNA and RNA}
 \begin{center} 
\includegraphics[width=0.5\linewidth]{rysunki/rys_1.pdf}
\end{center}
\end{frame}

\begin{frame}
  \frametitle{DNA and RNA}
 \begin{center} 
\includegraphics[width=0.5\linewidth]{rysunki/rys_2.png}
\end{center}
\end{frame}

\begin{frame}
  \frametitle{The standard genetic code}
 \begin{center} 
\includegraphics[width=0.5\linewidth]{rysunki/rys_3.png}
\end{center}
\end{frame}  

\begin{frame}
\frametitle{The Central Dogma of Genetics}
 \begin{center} 
\includegraphics[width=0.8\linewidth]{rysunki/rys_4.png}
\end{center}


\end{frame}  

\end{document}




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